Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_010959750.1 MCA_RS01930 aspartate kinase
Query= BRENDA::O69077 (412 letters) >NCBI__GCF_000008325.1:WP_010959750.1 Length = 409 Score = 590 bits (1520), Expect = e-173 Identities = 303/405 (74%), Positives = 348/405 (85%), Gaps = 2/405 (0%) Query: 1 MALIVQKFGGTSVGTVERIEQVAEKVKKFREAGDDVVVVVSAMSGETNRLIGLANQIMEQ 60 MAL V K+GGTSVG+ ERI+ VA+ V + R GDD++VVVSAMSGETNRL+ LA+++ E+ Sbjct: 1 MALFVHKYGGTSVGSPERIKNVAKNVIRARSRGDDIIVVVSAMSGETNRLVALAHEMHER 60 Query: 61 PVPRELDVMVSTGEQVTIALLSMALIKRGVPAVSYTGNQVRILTDSAHTKARILHIDDTH 120 P RE+DV+++TGEQVTIALLSMAL G PA SYTG QVRILTD AHTKARIL ID Sbjct: 61 PSTREMDVLLATGEQVTIALLSMALEAAGCPACSYTGGQVRILTDDAHTKARILDIDTDR 120 Query: 121 IRADLKAGRVVVVAGFQGVDGNGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180 IR+DL AGRVVVVAGFQG+ G+ITTLGRGGSDTT VALAAALKADEC IYTDVDGVYT Sbjct: 121 IRSDLAAGRVVVVAGFQGITEAGDITTLGRGGSDTTAVALAAALKADECLIYTDVDGVYT 180 Query: 181 TDPRVVPQARRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFQEGPGTLI 240 TDPR+ P+ARRLD+ITFEEMLEMASLGSKVLQIR+VEFAGKYNVPLRVL SF GPGTLI Sbjct: 181 TDPRIEPKARRLDRITFEEMLEMASLGSKVLQIRSVEFAGKYNVPLRVLSSFAAGPGTLI 240 Query: 241 TIDDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQNVA 300 T EE S+E+P+ISGIAFNRDEAKLT++GVPD PGVA++ILGP++ AN+EVDMIVQNVA Sbjct: 241 TY--EEASVEKPLISGIAFNRDEAKLTVKGVPDKPGVAYQILGPVAHANIEVDMIVQNVA 298 Query: 301 HDNTTDFTFTVHRNDYLNALEILKQTAANIGAREAIGDTNIAKVSIVGVGMRSHAGVASR 360 D TTDFTFTVHRNDY AL+IL+ T +GARE GD I KVS+VGVGMRSHAG+A+R Sbjct: 299 EDATTDFTFTVHRNDYRKALDILQATCTALGAREVTGDDKIVKVSLVGVGMRSHAGIAAR 358 Query: 361 MFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELD 405 MFEALA+E INI+MISTSEIK+S+V++EKYLELAVR LH AF LD Sbjct: 359 MFEALAREGINIRMISTSEIKISIVVDEKYLELAVRTLHEAFNLD 403 Lambda K H 0.317 0.133 0.362 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 540 Number of extensions: 14 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 412 Length of database: 409 Length adjustment: 31 Effective length of query: 381 Effective length of database: 378 Effective search space: 144018 Effective search space used: 144018 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
Align candidate WP_010959750.1 MCA_RS01930 (aspartate kinase)
to HMM TIGR00657 (aspartate kinase (EC 2.7.2.4))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR00657.hmm # target sequence database: /tmp/gapView.17256.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00657 [M=442] Accession: TIGR00657 Description: asp_kinases: aspartate kinase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-142 461.7 4.0 2.4e-139 451.2 4.0 2.0 1 lcl|NCBI__GCF_000008325.1:WP_010959750.1 MCA_RS01930 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000008325.1:WP_010959750.1 MCA_RS01930 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 451.2 4.0 2.4e-139 2.4e-139 1 441 [. 1 401 [. 1 402 [. 0.97 Alignments for each domain: == domain 1 score: 451.2 bits; conditional E-value: 2.4e-139 TIGR00657 1 maliVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseeekelieki 69 mal V K+GGtSvg+ erik+vak v++++ g++ +VVvSAm+g T++Lv+la+++++++ lcl|NCBI__GCF_000008325.1:WP_010959750.1 1 MALFVHKYGGTSVGSPERIKNVAKNVIRARSRGDDIIVVVSAMSGETNRLVALAHEMHERP-------- 61 7899*********************************************************........ PP TIGR00657 70 rekhlealeelasqalkeklkallekeleevkkereldlilsvGEklSaallaaaleelgvkavsllga 138 s re+d++l++GE++++all++ale+ g+ a s++g+ lcl|NCBI__GCF_000008325.1:WP_010959750.1 62 ------------S--------------------TREMDVLLATGEQVTIALLSMALEAAGCPACSYTGG 98 ............5....................79********************************** PP TIGR00657 139 eagiltdsefgrAkvleeikterleklleegiivvvaGFiGatekgeittLGRGGSDltAallAaalkA 207 + iltd+++++A+ + +i+t+r+ + l +g +vvvaGF+G+te g+ittLGRGGSD+tA++lAaalkA lcl|NCBI__GCF_000008325.1:WP_010959750.1 99 QVRILTDDAHTKAR-ILDIDTDRIRSDLAAGRVVVVAGFQGITEAGDITTLGRGGSDTTAVALAAALKA 166 **************.****************************************************** PP TIGR00657 208 deveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpe 276 de+ iytDVdG+yt+DPri p+Arrld i++eE+lE+aslG+kvL+ r++e+a ++++p++v s+f lcl|NCBI__GCF_000008325.1:WP_010959750.1 167 DECLIYTDVDGVYTTDPRIEPKARRLDRITFEEMLEMASLGSKVLQIRSVEFAGKYNVPLRVLSSFAAG 235 *******************************************************************99 PP TIGR00657 277 aeGTlivakskseeepavkalsldknqalvsvsgttmkpgilaevfgalaeakvnvdlilqsssets.. 343 +GTli+ ++ s e+p ++++++++++a+++v+g+++kpg++ +++g +a+a+++vd+i+q++ e+ lcl|NCBI__GCF_000008325.1:WP_010959750.1 236 -PGTLITYEEASVEKPLISGIAFNRDEAKLTVKGVPDKPGVAYQILGPVAHANIEVDMIVQNVAEDAtt 303 .********999999*************************************************66556 PP TIGR00657 344 .isfvvdkedadkakellkkkvkeekaleevevekklalvslvGagmksapgvaakifeaLaeeninie 411 +f+v+++d+ ka +l+ ++ ++ a +ev+ ++k+ +vslvG gm+s+ g+aa++feaLa+e+ini+ lcl|NCBI__GCF_000008325.1:WP_010959750.1 304 dFTFTVHRNDYRKALDILQATCTALGA-REVTGDDKIVKVSLVGVGMRSHAGIAARMFEALAREGINIR 371 8****************9876666665.57*************************************** PP TIGR00657 412 missseikisvvvdekdaekavealheklv 441 mis+seikis+vvdek+ e av++lhe++ lcl|NCBI__GCF_000008325.1:WP_010959750.1 372 MISTSEIKISIVVDEKYLELAVRTLHEAFN 401 ***************************995 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (442 nodes) Target sequences: 1 (409 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.04 # Mc/sec: 3.68 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory